Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:08:24 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for singleCellTK on machv2


To the developers/maintainers of the singleCellTK package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/singleCellTK.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1807/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singleCellTK 2.4.0  (landing page)
Yichen Wang
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/singleCellTK
git_branch: RELEASE_3_14
git_last_commit: 91f98fc
git_last_commit_date: 2021-10-27 11:24:49 -0500 (Wed, 27 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: singleCellTK
Version: 2.4.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singleCellTK_2.4.0.tar.gz
StartedAt: 2022-01-23 18:17:39 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 18:35:55 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 1096.8 seconds
RetCode: 0
Status:   OK  
CheckDir: singleCellTK.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singleCellTK_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/singleCellTK.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘2.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘singleCellTK’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   1.5Mb
    shiny     2.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  'AnnotationDbi' 'RColorBrewer'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
importExampleData        25.986  2.120  29.832
plotDoubletFinderResults 26.974  0.157  27.161
plotScDblFinderResults   23.235  0.534  23.800
runDoubletFinder         19.168  0.052  19.245
runScDblFinder           15.472  0.326  15.814
plotBatchCorrCompare     12.102  0.100  12.198
plotMarkerDiffExp        11.799  0.037  11.846
plotScdsHybridResults    11.713  0.107  11.822
plotBcdsResults          10.891  0.246  11.149
findMarkerDiffExp        10.385  0.097  10.489
plotDEGHeatmap            9.931  0.115  10.057
findMarkerTopTable        9.807  0.052   9.870
runDESeq2                 9.759  0.041   9.812
plotEmptyDropsResults     9.673  0.021   9.704
plotEmptyDropsScatter     9.602  0.020   9.632
plotDecontXResults        9.496  0.064   9.572
runEmptyDrops             9.169  0.013   9.189
runDecontX                7.747  0.020   7.774
plotCxdsResults           7.450  0.048   7.500
runMAST                   7.251  0.044   7.300
plotDEGViolin             6.989  0.103   7.098
detectCellOutlier         6.557  0.232   6.795
plotUMAP                  6.464  0.048   6.516
importGeneSetsFromMSigDB  6.105  0.308   6.423
plotDEGRegression         6.204  0.039   6.247
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.



Installation output

singleCellTK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL singleCellTK
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘singleCellTK’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (singleCellTK)

Tests output

singleCellTK.Rcheck/tests/spelling.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if (requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.310   0.073   0.358 

singleCellTK.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(singleCellTK)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: SingleCellExperiment
Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'DelayedArray'

The following objects are masked from 'package:base':

    aperm, apply, rowsum, scale, sweep


Attaching package: 'singleCellTK'

The following object is masked from 'package:BiocGenerics':

    plotPCA

> 
> test_check("singleCellTK")
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 0 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Shrinkage off - using GLM estimates for parameters
Adjusting the data
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 1 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Shrinkage off - using GLM estimates for parameters
Adjusting the data
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
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  |======================================================================| 100%
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Estimating GSVA scores for 34 gene sets.
Estimating ECDFs with Gaussian kernels

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Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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  |======================================================================| 100%
[18:33:20] WARNING: amalgamation/../src/learner.cc:1115: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
[18:33:23] WARNING: amalgamation/../src/learner.cc:1115: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
[18:33:49] WARNING: amalgamation/../src/learner.cc:1115: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
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  |======================================================================| 100%
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 390
Number of edges: 9849

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.8351
Number of communities: 7
Elapsed time: 0 seconds
Error in x$.self$finalize() : attempt to apply non-function
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 0 | WARN 15 | SKIP 0 | PASS 126 ]

[ FAIL 0 | WARN 15 | SKIP 0 | PASS 126 ]
> 
> proc.time()
   user  system elapsed 
319.997   4.542 326.450 

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.0030.0010.004
SEG0.0020.0020.004
calcEffectSizes0.3380.0080.346
combineSCE3.7160.0163.734
computeZScore0.5660.0240.591
convertSCEToSeurat4.5680.1534.730
convertSeuratToSCE1.0740.0971.172
dedupRowNames0.1320.0130.144
detectCellOutlier6.5570.2326.795
diffAbundanceFET0.0690.0020.071
discreteColorPalette0.0080.0000.008
distinctColors0.0030.0000.003
downSampleCells1.3420.0841.426
downSampleDepth1.1250.0361.163
enrichRSCE0.7500.0272.423
exportSCE0.0020.0030.005
exportSCEtoAnnData0.2100.0070.217
exportSCEtoFlatFile0.2190.0040.222
featureIndex0.0350.0040.038
findMarkerDiffExp10.385 0.09710.489
findMarkerTopTable9.8070.0529.870
generateSimulatedData0.0660.0040.070
getBiomarker0.0540.0010.055
getDEGTopTable1.4970.0111.510
getMSigDBTable0.0050.0030.008
getTSNE0.6880.0080.697
getTopHVG0.5310.0050.537
getUMAP4.3800.0474.422
importAnnData0.0010.0000.001
importBUStools0.6360.0030.641
importCellRanger2.4050.0492.461
importCellRangerV2Sample0.6530.0040.658
importCellRangerV3Sample0.8610.0130.876
importDropEst0.8240.0070.831
importExampleData25.986 2.12029.832
importGeneSetsFromCollection1.3860.0941.482
importGeneSetsFromGMT0.1000.0030.103
importGeneSetsFromList0.3370.0050.342
importGeneSetsFromMSigDB6.1050.3086.423
importMitoGeneSet0.1080.0060.114
importOptimus0.0010.0010.002
importSEQC0.5940.0030.599
importSTARsolo0.6850.0030.690
iterateSimulations1.1180.0081.127
mergeSCEColData1.0940.0171.113
mouseBrainSubsetSCE0.0010.0020.004
msigdb_table0.0020.0020.002
plotBarcodeRankDropsResults1.9990.0132.015
plotBarcodeRankScatter1.6560.0071.665
plotBatchCorrCompare12.102 0.10012.198
plotBatchVariance0.5340.0480.584
plotBcdsResults10.891 0.24611.149
plotClusterAbundance1.1330.0281.166
plotCxdsResults7.4500.0487.500
plotDEGHeatmap 9.931 0.11510.057
plotDEGRegression6.2040.0396.247
plotDEGViolin6.9890.1037.098
plotDecontXResults9.4960.0649.572
plotDimRed0.6250.0060.633
plotDoubletFinderResults26.974 0.15727.161
plotEmptyDropsResults9.6730.0219.704
plotEmptyDropsScatter9.6020.0209.632
plotMASTThresholdGenes3.2440.0163.263
plotMarkerDiffExp11.799 0.03711.846
plotPCA1.1940.0091.205
plotRunPerCellQCResults0.0030.0010.003
plotSCEBarAssayData0.2070.0010.209
plotSCEBarColData0.1770.0020.179
plotSCEBatchFeatureMean0.3100.0040.315
plotSCEDensity0.3200.0030.323
plotSCEDensityAssayData0.2550.0020.258
plotSCEDensityColData0.3340.0020.337
plotSCEDimReduceColData1.6380.0151.660
plotSCEDimReduceFeatures0.7580.0040.763
plotSCEHeatmap1.5490.0071.558
plotSCEScatter0.7390.0050.747
plotSCEViolin0.3060.0030.312
plotSCEViolinAssayData0.3450.0040.350
plotSCEViolinColData0.3550.0030.359
plotScDblFinderResults23.235 0.53423.800
plotScdsHybridResults11.713 0.10711.822
plotScrubletResults0.0020.0010.004
plotTSNE1.2150.0071.223
plotTopHVG0.8700.0080.878
plotUMAP6.4640.0486.516
readSingleCellMatrix0.0040.0010.005
reportCellQC0.4820.0030.485
reportDropletQC0.0020.0010.004
reportQCTool0.4600.0030.463
retrieveSCEIndex0.0200.0010.021
runANOVA2.4830.0132.500
runBBKNN0.0000.0010.001
runBarcodeRankDrops1.1800.0051.189
runBcds3.9200.0283.954
runCellQC0.3730.0020.375
runComBatSeq0.9230.0170.940
runCxds1.2580.0281.287
runCxdsBcdsHybrid4.3570.0234.380
runDEAnalysis2.0730.0262.101
runDESeq29.7590.0419.812
runDecontX7.7470.0207.774
runDimReduce2.0200.0162.042
runDoubletFinder19.168 0.05219.245
runDropletQC0.0010.0000.002
runEmptyDrops9.1690.0139.189
runFastMNN3.2160.0263.250
runFeatureSelection0.3980.0010.400
runGSVA1.7280.0111.740
runKMeans1.1820.0071.191
runLimmaBC0.1970.0010.199
runLimmaDE1.8220.0071.831
runMAST7.2510.0447.300
runMNNCorrect1.3830.0041.387
runNormalization3.0680.0263.099
runPerCellQC0.8890.0050.896
runSCANORAMA0.0010.0000.001
runSCMerge0.0020.0000.002
runScDblFinder15.472 0.32615.814
runScranSNN1.1770.0081.186
runScrublet0.0010.0000.002
runSingleR0.0970.0040.100
runVAM1.5570.0251.585
runWilcox1.8630.0071.870
runZINBWaVE0.0030.0010.003
sampleSummaryStats0.8720.0030.875
scaterCPM0.3550.0140.392
scaterPCA1.4450.0071.453
scaterlogNormCounts1.7730.0121.786
sce0.0020.0030.005
scranModelGeneVar0.4790.0090.489
sctkListGeneSetCollections0.3940.0100.404
sctkPythonInstallConda000
sctkPythonInstallVirtualEnv000
selectSCTKConda0.0000.0000.001
selectSCTKVirtualEnvironment0.0000.0000.001
setSCTKDisplayRow0.7540.0110.765
seuratComputeHeatmap0.0020.0010.003
seuratComputeJackStraw0.0030.0010.004
seuratElbowPlot0.0020.0010.004
seuratFindClusters0.0020.0010.004
seuratFindHVG0.0030.0010.003
seuratICA0.0020.0010.004
seuratJackStrawPlot0.0020.0010.004
seuratNormalizeData0.0020.0010.003
seuratPCA0.0020.0000.002
seuratPlotHVG0.0010.0010.002
seuratReductionPlot0.0030.0020.003
seuratRunUMAP0.0020.0020.004
seuratSCTransform4.5160.0614.584
seuratScaleData0.0030.0010.004
singleCellTK0.0000.0000.001
subDiffEx1.1090.0111.121
subsetSCECols0.4700.0040.475
subsetSCERows1.1570.0171.175
summarizeSCE0.1170.0030.122
trimCounts0.5520.0140.567